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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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Error in in CreateSeuratObject when running cbSeurat on an expression matrix #238

Closed bugacov closed 2 years ago

bugacov commented 2 years ago

Hi, I'm trying to run cbSeurat on an expression matrix and keep getting this error on in CreateSeuratObject(..). I downloaded your example from adultPancreas matrix and tried running it and get the same error than when running my matrix.

adultPancreas% ls -l total 22396 -rw-r--r--. 1 root root 22707068 Feb 27 2019 exprMatrix.tsv.gz -rw-r--r--. 1 root root 522326 Apr 2 2020 meta.tsv adultPancreas% cbSeurat --exprMatrix=exprMatrix.tsv.gz --name=myDataset --outDir=seurat-out WARNING:root:seurat.conf not found, using default values for all Seurat options. Use --init to create a sample file. INFO:root:Creating seurat-out INFO:root:Wrote R script to seurat-out/runSeurat.R INFO:root:running seurat-out/runSeurat.R through Rscript Loading required package: R.methodsS3 R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help. R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help. R version 4.0.5 (2021-03-31) Seurat loaded, version 4.1.0 [1] "Seurat: Reading data" [1] "Seurat: Reading data" [1] "Loading input data matrix" NULL [1] "Loading tsv file with read.delim" [1] "Seurat: Setup" Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes = 200) : argument "counts" is missing, with no default Execution halted

real 0m51.316s user 0m44.770s sys 0m3.390s INFO:root:Wrote logfile of R run to seurat-out/analysisLog.txt ERROR:root:R script did not complete successfully. Check seurat-out/runSeurat.R and analysisLog.txt.

maximilianh commented 2 years ago

Yes, Seurat4 is not supported yet by this script. At UCSC, we're still on Seurat 3. I'm working today on adding it, give me a few hours...

On Wed, Mar 30, 2022 at 1:33 AM bugacov @.***> wrote:

Hi, I'm trying to run cbSeurat on an expression matrix and keep getting this error on in CreateSeuratObject(..). I downloaded your example from adultPancreas matrix and tried running it and get the same error than when running my matrix.

adultPancreas% ls -l total 22396 -rw-r--r--. 1 root root 22707068 Feb 27 2019 exprMatrix.tsv.gz -rw-r--r--. 1 root root 522326 Apr 2 2020 meta.tsv adultPancreas% cbSeurat --exprMatrix=exprMatrix.tsv.gz --name=myDataset --outDir=seurat-out WARNING:root:seurat.conf not found, using default values for all Seurat options. Use --init to create a sample file. INFO:root:Creating seurat-out INFO:root:Wrote R script to seurat-out/runSeurat.R INFO:root:running seurat-out/runSeurat.R through Rscript Loading required package: R.methodsS3 R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help. R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help. R version 4.0.5 (2021-03-31) Seurat loaded, version 4.1.0 [1] "Seurat: Reading data" [1] "Seurat: Reading data" [1] "Loading input data matrix" NULL [1] "Loading tsv file with read.delim" [1] "Seurat: Setup" Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes = 200) : argument "counts" is missing, with no default Execution halted

real 0m51.316s user 0m44.770s sys 0m3.390s INFO:root:Wrote logfile of R run to seurat-out/analysisLog.txt ERROR:root:R script did not complete successfully. Check seurat-out/runSeurat.R and analysisLog.txt.

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bugacov commented 2 years ago

Hi, Thanks for your reply. Lmk if you were able to make those changes and how should I update my code to get the fix. Also, I'm not sure that familiar with R but don't know how to get the code to use Seurat 3. I've tried going into R and deleting the Seurat package and then adding Seurat version 3.2.2 but then when the cbSeurat code runs it always uses Seurat version 4. So not sure how to force your code to use Seurat 3. Thanks! Alejandro.

From: Maximilian Haeussler @.> Sent: Wednesday, March 30, 2022 4:54 AM To: maximilianh/cellBrowser @.> Cc: Alejandro Bugacov @.>; Author @.> Subject: Re: [maximilianh/cellBrowser] Error in in CreateSeuratObject when running cbSeurat on an expression matrix (Issue #238)

Yes, Seurat4 is not supported yet by this script. At UCSC, we're still on Seurat 3. I'm working today on adding it, give me a few hours...

On Wed, Mar 30, 2022 at 1:33 AM bugacov @.***> wrote:

Hi, I'm trying to run cbSeurat on an expression matrix and keep getting this error on in CreateSeuratObject(..). I downloaded your example from adultPancreas matrix and tried running it and get the same error than when running my matrix.

adultPancreas% ls -l total 22396 -rw-r--r--. 1 root root 22707068 Feb 27 2019 exprMatrix.tsv.gz -rw-r--r--. 1 root root 522326 Apr 2 2020 meta.tsv adultPancreas% cbSeurat --exprMatrix=exprMatrix.tsv.gz --name=myDataset --outDir=seurat-out WARNING:root:seurat.conf not found, using default values for all Seurat options. Use --init to create a sample file. INFO:root:Creating seurat-out INFO:root:Wrote R script to seurat-out/runSeurat.R INFO:root:running seurat-out/runSeurat.R through Rscript Loading required package: R.methodsS3 R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help. R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help. R version 4.0.5 (2021-03-31) Seurat loaded, version 4.1.0 [1] "Seurat: Reading data" [1] "Seurat: Reading data" [1] "Loading input data matrix" NULL [1] "Loading tsv file with read.delim" [1] "Seurat: Setup" Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes = 200) : argument "counts" is missing, with no default Execution halted

real 0m51.316s user 0m44.770s sys 0m3.390s INFO:root:Wrote logfile of R run to seurat-out/analysisLog.txt ERROR:root:R script did not complete successfully. Check seurat-out/runSeurat.R and analysisLog.txt.

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maximilianh commented 2 years ago

Sorry for the delay. This should be now fixed in the develop branch. Can you clone that and try it there? Otherwise I can make pip prerelease for you that you can install with pip --pre.

bugacov commented 2 years ago

I tested it from the clone I made and seems to be working fine!! I'd really appreciate if you can do a pip prerelease!!! Thanks!

maximilianh commented 2 years ago

OK, I've fixed a few other things around cbSeurat (I don't think we're still using it here, I mostly use cbScanpy now). You can install a prerelease of 1.2 with

pip install cellbrowser --pre

Let me know if you run into problems. We hope to release this version within 1-2 weeks.

On Wed, Apr 6, 2022 at 5:24 AM bugacov @.***> wrote:

I tested it from the clone I made and seems to be working fine!! I'd really appreciate if you can do a pip prerelease!!! Thanks!

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